Package index • BIOMASS

Estimate above ground biomass (ABG) and its uncertainty

The following functions aim to retrieve compulsory parameters such as wood density and tree height, which lead to the final estimate of the AGB and its uncertainty

Correct tree taxonomy

correctTaxo(): Correct and match taxonomic names to the World Flora Online database
subPattern(): Common taxonomic name substitutions

Estimate wood density

getWoodDensity(): Estimating wood density and associated uncertainties

Estimate tree height

modelHD(): Fitting height-diameter models
retrieveH(): Retrieving tree height from models

Estimate AGB

computeAGB(): Computing tree above ground biomass (AGB)

Propagate uncertainties

AGBmonteCarlo(): Propagating above ground biomass (AGB) or carbon (AGC) errors to the stand level

Summarise at stand level

summaryByPlot(): Summarise by plot the posterior distribution of AGB values

Spatialized trees and forest stand metrics

Check plot coordinates

check_plot_coord(): Check coordinates of plot corners and trees

Divide plot into subplots

divide_plot(): Divides one ore more plots into subplots

subplot_summary(): Summarise and display tree information by subplot

Predict AGBD map based on inventory and LiDAR data

Calibrate AGBD-LiDAR log-log model

calibrate_model(): Calibrate a bayesian model to fit log(AGBD) ~ log(raster metric)

Predict AGBD map based on calibrated model

predict_map(): Predict map of AGBD and associated uncertainty

Other functions

bilinear_interpolation(): Generalized bilinear interpolation of coordinates
procrust(): Procrust analysis

latlong2UTM(): Translate the long lat coordinate in UTM coordinate

Retrieve Feldpausch regions

computeFeldRegion(): Retrieving Feldpausch regions

Predict tree height from a HD-model

predictHeight(): Tree height predictions

Manage user cache

cacheManager(): Function that return a possibly cached file, transparently downloading it if missing
cachePath(): Function used to build a file path based on a cache folder
createCache(): Function used to create or activate a permanent cache.
clearCache(): Function to clear cache content and possibly remove it

Documentation

Methods used for modeling height-diameter relationship

loglogFunction() michaelisFunction() weibullFunction(): HDmethods

Datasets

The four datasets used for examples and vignettes

NouraguesHD: Height-Diameter data
NouraguesCoords: Nouragues plot coordinates
NouraguesPlot201: Nouragues plot 201 coordinates
NouraguesTrees: Nouragues forest dataset

Deprecated functions

These functions are deprecated and will be removed in the version 3.0

attributeTree() deprecated: Attribute trees to subplots
attributeTreeCoord() deprecated: Attribute GPS coordinates to trees
correctCoordGPS() deprecated: Correct the GPS coordinates
cutPlot() deprecated: Divides one or more plots into subplots
numberCorner() deprecated: Get the UTM coordinates with the corner of the plot
getTaxonomy() deprecated: Retrieve trees taxonomy